>I need to have both versions and I must convert or recreate source file everytime I switch the version.
>How could I solve this problem?

Since it's VFP and FPDOS they each have a different name for the CONFIG file they use.

In VFP's CONFIG.FPW:
RESOURCE=VFPUSER

In FPDOS's CONFIG.FP:
RESOURCE=DOSUSER

This will use different resource files than the standard FOXUSER.DBF that's the default resource file.